Beta-galactosidase derived from bacillus circulans

ABSTRACT

Disclosed is a novel β-galactosidase. Specifically disclosed are a β-galactosidase derived from  Bacillus circulans  and a gene for the β-galactosidase. The β-galactosidase can be used, for example, in the production of milk, dairy products, fermented dairy products, galacto-oligosaccharides or supplements for foods.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional application of U.S. application Ser. No. 13/375,860 filed Dec. 2, 2011 which application is the U.S. national phase, pursuant to 35 U.S.C. §371, of PCT/JP2010/057204 filed Apr. 23, 2010, designating the United States and published in Japanese on Dec. 9, 2010 as publication WO 2010140435. PCT/JP2010/057204 claims priority to Japanese Patent Application Ser. No. 2009-136735, filed Jun. 5, 2009. The entire contents of the aforementioned patent applications are incorporated herein by reference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Dec. 2, 2011, is named AE09007Pamano_ST25.txt and is 68,988 bytes in size.

TECHNICAL FIELD

The present invention relates to a β-galactosidase. More particularly, the invention relates to a novel β-galactosidase isolated from Bacillus circulans, a gene thereof, and their use. For example, the β-galactosidase of the invention can be used in the production of low-lactose milks and galacto-oligosaccharides that are an intestinal Bifidobacterium growth factor, or can be used as an active ingredient for medicines or supplements in patients with lactose intolerance. The present application claims a priority date of Jun. 5, 2009 based on Japanese patent application No. 2009-136735, which is hereby incorporated by reference in its entirety.

BACKGROUND ART

Beta-galactosidase (EC3.2.1.23) is an enzyme that hydrolyzes the β-D-galactoside bond to release D-galactose, and, in general, it is widely distributed in microorganisms, and animals and plants. Beta-galactosidase is also referred to as lactase, and has been used as an enzyme for the production of a whey syrup from whey that is by-produced during the production of low-lactose milk for lactose intolerance or cheese, or as an active ingredient for medicines or supplements in patients with lactose intolerance. In addition, β-galactosidase has an ability to transfer the galactoside bond, and a method to prepare galacto-oligosaccharides (oligosaccharides with galactose residues) using this ability is known. Beta-galactosidases from a koji bacterium (Aspergillus oryzae), a yeast (Kluyveromyces lactis, Kluyveromyces marxinus), and a bacterium (Bacillus circulans) are known for use in these applications.

Among these, β-galactosidase derived from Bacillus circulans has been studied by Mozaffer et al. (non-patent document 1), Vetere et al. (non-patent document 2), and Ito et al. (non-patent documents 3 and 4). According to the non-patent document 1, purification of two kinds of enzymes each having a molecular weight of 240 kDa and 160 kDa is reported. It is further reported that the former has a high hydrolyzing activity, and the latter has a high transgalactosylation activity, and that the former showed a higher hydrolyzing activity against a synthetic substrate p-nitrophenyl-β-D-galactopyranoside (ONPG) than against lactose. On the other hand, according to the non-patent document 2, purification of three kinds of enzymes each having a molecular weight of 212 kDa, 145 kDa, and 86 kDa is reported. However, mutual protein chemical correlation and molecular biological characteristics (genetically) of these plural enzymes were not clear. In addition, in the non-patent documents 3 and 4, a gene cloning of the 67 kDa enzyme, and properties of the recombinant protein are reported, but the enzyme is specific to the β-1,3 bond, and does not act on the β-1,4 bond that is a bond of lactose present in a milk. Therefore, such an enzyme is different from the β-galactosidase ordinarily used in the treatment of milk or lactose derived from milk. In addition, two kinds of β-galactosidase genes derived from Bacillus circulans are registered at the GENBANK™ (GENBANK™ accession number of L03424 and L03425), but only gene sequences for these have been reported and it is not certain whether such genes encode actually an active protein.

PRIOR ART DOCUMENTS Non-Patent Documents

-   Non-patent document 1: Mozaffar, Z., Nakanishi, K., Matsuno, R., and     Kamikubo, T., Agric. Biol. Chem., 48(12), 3053-3061, 1984 -   Non-patent document 2: Vetere, A., and Paoletti, S. Biochem.     Biophys. Acta., 1380, 223-231 (1998) -   Non-patent document 3: Ito. Y., and Sasaki, T. Biosci. Biotech.     Biochem., 61(8), 1270-1276 (1997) -   Non-patent document 4: Fujimoto, H., Miyasato, M., Ito, Y., Sasaki,     T., and Ajisaka, K. Glycoconjugate Journal, 15, 155-160 (1998) -   Non-patent document 5: Saito, and Miura. Biochim. Biophys. Acta, 72,     619-629 (1963)

SUMMARY OF THE INVENTION Problems to be Solved by the Invention

Thus, plural enzymes have been reported as β-galactosidase derived from Bacillus circulans, but there was a limitation in the production of enzyme preparations suitable for respective industrial applications including the production of low-lactose milks and galacto-oligosaccharides because mutual protein chemical correlation and molecular biological characteristics (genetically) of these plural enzymes were not clear.

Means for Solving Problem

The present invention provides a novel β-galactosidase derived from Bacillus circulans. The present inventors have found an enzyme (referred to as “β-Gal1” in the present specification) having a molecular weight of 195 kDa (as estimated by SDS-PAGE 189.3 kDa by mass spectrometry) which has not been reported so far, in the course of studies on β-galactosidases produced by Bacillus circulans, and have succeeded in cloning of the gene that encodes said enzyme (hereinafter referred to as the present gene). In addition, the base sequence of the present gene and the deduced amino acid sequence are greatly different from those of three kinds of β-galactosidases derived from Bacillus circulans which have been reported so far (see the non-patent document 3 concerning the amino acid sequence, GENBANK™ accession No L03424 and L03425), and they were found to be novel. Moreover, the present inventors have found that Bacillus circulans produces three kinds of enzymes (hereinafter referred to as “β-Gal2”, “β-Gal3”, and “β-Gal4” in this specification) having a low hydrolyzing activity against a synthetic substrate 2-nitrophenyl β-D-galactopyranoside: ONPG, i.e. having a high transgalactosylation activity. Furthermore, it has also been found that these three kinds of β-galactosidases are produced from the present gene (a gene encoding β-Gal1). In addition, a method for producing a protein group of these β-galactosidases has been established by introducing the present gene and a fragment thereof into a suitable host. The invention has been completed based on the above results. The invention is shown as follows.

[1] A β-galactosidase derived from Bacillus circulans having a molecular weight of 195 kDa (by SDS-PAGE).

[2] A β-galactosidase derived from Bacillus circulans, including a fragment of the β-galactosidase according to [1].

[3] A β-galactosidase including the amino acid sequence of SEQ ID NO: 7 or its fragment showing a β-galactosidase activity.

[4] The β-galactosidase according to [3], wherein the fragment includes a region from the N-terminal to WSIGNEIY (SEQ ID NO: 18) of the amino acid sequence of SEQ ID NO: 7.

[5] The β-galactosidase according to [3], wherein the fragment includes the amino acid sequence of any one of SEQ ID NO: 8 to SEQ ID NO:10.

[6] The β-galactosidase according to [3], which is encoded by a DNA including the sequence of SEQ ID NO: 5.

[7] A β-galactosidase gene including any one of DNAs selected from the group consisting of the followings (a) to (e):

-   -   (a) DNA encoding the amino acid sequence of SEQ ID NO: 6 or 7;     -   (b) DNA including the sequence of SEQ ID NO: 5;     -   (c) DNA that hybridizes to the complementary sequence of the         sequence of SEQ ID NO: 5 under stringent conditions;     -   (d) DNA that is a degenerate DNA sequence of the sequence of SEQ         ID NO: 5; and     -   (e) DNA encoding a protein having a sequence which includes         substitution, deletion, insertion, addition or inversion in one         or a plurality of bases when the sequence of SEQ ID NO: 5 is a         reference sequence, and which has a β-galactosidase activity.

[8] The β-galactosidase gene according to [7], wherein the protein having a β-galactosidase activity includes the amino acid sequence of SEQ ID NO: 7 or its fragment, wherein changes in the amino acid sequence are occurred in less than 60%, preferably less than 45%, and further preferably less than 25%.

[9] The β-galactosidase gene according to [8], wherein the changes are a conservative amino acid substitution.

[10] A β-galactosidase, which is encoded by the β-galactosidase gene according to any one of [7] to [9].

[11] A recombinant vector including the β-galactosidase gene according to any one of [7] to [9].

[12] The recombinant vector according to [11], which is an expression vector.

[13] A transformant into which the β-galactosidase gene according to any one of [7] to [9] has been introduced.

[14] A transformant into which the recombinant vector according to [11] or [12] has been introduced.

[15] A transformant according to [13] or [14], which is a bacterial cell, a yeast cell or a fungal cell. [16] A method for producing a β-galactosidase, including the following steps of:

-   -   (1) culturing the transformant according to any one of [13] to         [15] under conditions such that a protein encoded by the         β-galactosidase gene is produced; and     -   (2) collecting the produced protein.

[17] An enzyme preparation including as an active ingredient the β-galactosidase according to any one of [1] to [6] and [10].

[18] The enzyme preparation according to [17], wherein the active ingredient is one or more β-galactosidases selected from the group consisting of β-galactosidase including the amino acid sequence of SEQ ID NO: 7, β-galactosidase including the amino acid sequence of SEQ ID NO: 8, β-galactosidase including the amino acid sequence of SEQ ID NO: 9, and β-galactosidase including the amino acid sequence of SEQ ID NO: 10.

[19] Use of the β-galactosidase of any one of [1] to [6] and [10] or the enzyme preparation of [17] or [18] for the production of a product selected from the group consisting of a low-lactose milk, a galacto-oligosaccharide that is an intestinal bifidobacterium growth factor, and a medicine or supplement for patients with lactose intolerance.

[20] A low-lactose milk, a galacto-oligosaccharide that is an intestinal bifidobacterium growth factor, and a medicine or supplement for patients with lactose intolerance, which are obtained by use of the β-galactosidase of any one of [1] to [6] and [10] or the enzyme preparation of [17] or [18].

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an elution pattern of a hydroxyapatite chromatography of a crude enzyme solution of β-galactosidase derived from Bacillus circulans. The absorbance at 280 nm corresponds to the protein and the absorbance at 420 nm measured by the ONPG method corresponds to the β-galactosidase activity, respectively.

FIG. 2 is an elution pattern of an affinity chromatography of the obtained fraction 1 (see FIG. 1). The absorbance at 280 nm corresponds to the protein concentration and the absorbance at 420 nm measured by the ONPG method corresponds to the β-galactosidase activity.

FIG. 3 is an elution pattern of an affinity chromatography of the obtained fraction 2 (see FIG. 1). The absorbance at 280 nm corresponds to the protein concentration and the absorbance at 420 nm measured by the ONPG method corresponds to the β-galactosidase activity.

FIG. 4 is the result of an SDS-polyacrylamide gel electrophoresis of four kinds of purified β-galactosidases including β-Gal1 (lane 3), β-Gal2 (lane 4), β-Gal3 (lane 5), and β-Gal4 (lane 6). A crude enzyme powder was provided to the lane 2. The molecular weight of a molecular weight marker (lanes 1 and 7) used is shown in the left end.

FIG. 5 is the result of an SDS-polyacrylamide gel electrophoresis of a centrifugal supernatant from the cell lysates of an Escherichia coli transformant. Lane 1 is β-Gal1, lane 2 is β-Gal2, lane 3 is β-Gal3, and lane 4 is β-Gal4. The lanes 5 and 6 are each a centrifugal supernatant from the cell lysates of a transformant transformed with an Escherichia coli vector. The arrow shows an expressed β-galactosidase protein. In the left end, the molecular weight of a molecular weight marker (lane M) used is shown.

TERMS

The term “DNA encoding amino acid sequence” in the present invention denotes DNA from which the protein having the amino acid sequence is obtained when it is expressed, that is, DNA having a base sequence corresponding to an amino acid sequence of the protein. Therefore, the codon degeneracy is also taken into consideration.

In the present specification, the term “isolated” and “purified” are used interchangeably. The term “isolated” used with respect to the enzyme of the present invention (β-galactosidase), which is derived from a natural material, denotes a state in which components other than the enzyme are not substantially contained (in particular, contaminated protein is not substantially contained) in the natural material. Specifically, in the isolated enzyme of the present invention, the content of the contaminant protein is, for example, less than about 20%, preferably less than about 10%, further preferably less than about 5%, and yet further preferably less than about 1% with respect to the total amount on the weight basis. On the other hand, the term “isolated” when the enzyme of the present invention is prepared by genetically engineering technique denotes a state in which other components derived from a host cell to be used, a culture solution, and the like, are not substantially contained. Specifically, for example, in the isolated enzyme of the present invention, the content of the contaminant components is less than about 20%, preferably less than about 10%, further preferably less than about 5%, and yet further preferably less than about 1% with respect to the total amount on the weight basis. Unless otherwise specified, when merely the term “β-galactosidase” is used in this specification, it signifies the “β-galactosidase in an isolated state.” The same is true to the term “the present enzyme” used instead of β-galactosidase.

The term “isolated” used with respect to DNA denotes typically that DNA is separated from other nucleic acid coexisting in nature when the DNA originally exists in nature. However, some of the other nucleic acid components such as a neighboring nucleic acid sequence in nature (for example, a sequence of a promoter region, a terminator sequence, or the like) may be included. For example, in the “isolated” state of the genome DNA, the isolated DNA preferably does not substantially include other DNA components coexisting in nature. On the other hand, in the “isolated” state of DNA prepared by a genetic engineering technique, for example, a cDNA molecule, and the like, preferably, the DNA does not substantially include cell components, a culture solution, or the like. Similarly, in the “isolated” state in the case of DNA prepared by chemical synthesis, the DNA does not include a precursor (a raw material) or chemical materials used in synthesis, for example, dNTP. Unless otherwise specified, when merely the term “DNA” is used in this specification, it signifies the “DNA in an isolated state.”

In general, β-galactosidase shows a lactose hydrolyzing activity (an activity to hydrolyze lactose by the action on the β-1,4 bond) and a transgalactosylation activity (an activity to transfer galactose). Therefore the “β-galactosidase activity” in the invention is intended to include such two activities. The lactose hydrolyzing activity can be measured by the lactose method described in Examples. The other transgalactosylation activity can be expressed by using an index of the ratio of the activity value by the ONPG method shown in Examples/the activity value by the lactose method shown in Examples. It is known that the transgalactosylation activity becomes higher when the ratio of the activity value by the ONPG method shown in Examples/the activity value by the lactose method shown in Examples becomes smaller (non-patent document 1).

The “molecular weight” in the present invention means, unless otherwise indicated, a molecular weight measured by an SDS-PAGE (SDS-polyacrylamide gel electrophoresis).

(β-Galactosidase)

The first aspect of the invention provides a Bacillus circulans-derived β-galactosidase that has been successfully isolated and characterized by the present inventors. In one embodiment of the invention, the molecular weight of the β-galactosidase is 195 kDa (by SDS-PAGE). In the course of isolation and purification of the β-galactosidase, the present inventors have found that β-galactosidase (β-Gal2) with a molecular weight of 135 kDa, β-galactosidase (β-Gal3) of 86 kDa, and β-galactosidase (β-Gal4) of 160 kDa (each by SDS-PAGE) are produced, and also have found that these three kinds of β-galactosidases are all derived from one gene. On the other hand, it was confirmed that a gene in which a half or more of the C-terminal region was deleted expressed an active β-galactosidase. Based on these findings, another embodiment of the invention provides a β-galactosidase including a fragment (hereinafter referred to as the present fragment) of the above β-galactosidase (β-galactosidase with a molecular weight of 195 kDa, derived from Bacillus circulans). The length of the present fragment is not particularly limited as long as the present fragment shows a β-galactosidase activity, but it contains, for example, 5 to 98% protein, preferably 40 to 95% protein, and most preferably 55 to 75% protein relative to a standard protein. In addition, the present fragment preferably includes an N-terminal region of the standard protein. Specific examples of the present fragment are β-galactosidase (β-Gal2) having a molecular weight of 135 kDa, β-galactosidase (β-Gal3) having a molecular weight of 86 kDa, and β-galactosidase (β-Gal4) having a molecular weight of 160 kDa, all of which have been discovered by the present inventors.

The present fragment can also be obtained by a protease treatment. For example, the present fragment can be obtained by subjecting the purified β-galactosidase (β-galactosidase having a molecular weight of 195 kDa, derived from Bacillus circulans) to a protease treatment. Alternatively, the present fragment including the above β-galactosidase may be obtained by treating a culture solution of Bacillus circulans with a protease. There is no particular limitation to the protease used. For example, a commercially available protease preparation or an endogenous protease produced by Bacillus circulans can be used.

In one embodiment, the β-galactosidase of the invention includes the amino acid sequence of SEQ ID NO: 7. The amino acid sequence is formed by removing the signal peptide moiety from the amino acid sequence of SEQ ID NO: 6. In addition, the amino acid sequence of SEQ ID NO: 6 is an amino acid sequence that is deduced from the base sequence (SEQ ID NO: 5) of a gene obtained by cloning from Bacillus circulans. The β-galactosidase of the invention having the amino acid sequence of SEQ ID NO: 7 is a novel enzyme that is clearly different from three kinds of β-galactosidases derived from Bacillus circulans which have been reported so far, because of difference in the number of the amino acids and low homology (10 to 12%).

Other embodiment of the invention is a β-galactosidase including a fragment having the amino acid sequence of SEQ ID NO: 7. Herein, the fragment contains a region from the N-terminal to WSIGNEIY (SEQ ID NO: 18) of the amino acid sequence of SEQ ID NO: 7. The moiety sequence (WSIGNEIY) is a putative active domain. A specific example of the fragment can include those having an amino acid sequence of any one of SEQ ID NO: 8 to SEQ ID NO: 10. The amino acid sequence of SEQ ID NO: 8 corresponds to Gal2, the amino acid sequence of SEQ ID NO: 9 corresponds to Gal3, and the amino acid sequence of SEQ ID NO: 10 corresponds to Gal4.

Generally, when a part of an amino acid sequence of a certain protein is modified, the modified protein may have the equal function to that of the protein before the modification. That is to say, the modification of the amino acid sequence may not have a substantial effect on the function of the protein, so that the function of the protein may be maintained before and after the modification. When this technical common sense is considered, an enzyme that has a recognizable slight difference in the amino acid sequence and has no substantially recognizable difference in the function as β-galactosidase can be regarded as an enzyme that is substantially the same as the above β-galactosidase in comparison with β-galactosidase (including any one of the amino acid sequences of SEQ ID NO: 7 to SEQ ID NO: 10) of the invention. The term “slight difference in the amino acid sequence” as used herein typically means that the amino acid sequence is mutated (changed) by the deletion or substitution of one to several amino acids (the upper limit: e.g. 3, 5, 7, or 10 amino acids) constituting the amino acid sequence, or by the addition, insertion, or combination thereof, of one to several amino acids (the upper limit: e.g. 3, 5, 7, or 10 amino acids). The identity (%) of between the amino acid sequence in the “substantially the same enzyme” and the amino acid sequence of the above β-galactosidase as a standard is preferably 90% or more, more preferably 95% or more, yet more preferably 98% or more, and most preferably 99% or more. In addition, the difference in the amino acid sequence may occur in a plurality of positions.

The “slight difference in the amino acid sequences” is preferably generated by a conservative amino acid substitution. Herein, the “conservative amino acid substitution” is a substitution in which the amino acid residue is substituted with an amino acid residue having a side chain with similar feature. The amino acid residues are divided into some families depending on side chains thereof, including basic side chains (e g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine), and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). The conservative amino acid substitution is preferably a substitution between amino acid residues of the same family.

The identity (%) between two amino acid sequences can be determined by the following procedure. Firstly, two sequences are aligned for optimum comparison of the two sequences (for example, a gap may be introduced into the first sequence so as to optimize the alignment with respect to the second sequence). When a molecule (amino acid residue) at a specific position in the first sequence and a molecule in the corresponding position in the second sequence are the same as each other, the molecules in the positions are defined as being identical. The identity between two sequences is a function of the number of identical positions shared by the two sequences (i.e., identity (%)=number of identical positions/total number of positions×100). Preferably, the number and size of the gaps, which are required to optimize the alignment of the two sequences, are taken into consideration.

The comparison and determination of the identity between two sequences can be carried out by using a mathematical algorithm. A specific example of the mathematical algorithm that can be used for comparing the sequences includes an algorithm described in Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264-68 and modified by Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-77. However, the algorithm is not necessarily limited to this. Such an algorithm is incorporated in NBLAST program and XBLAST program (version 2.0) described in Altschul et al. (1990) J. Mol. Biol. 215: 403-10. In order to obtain an amino acid sequence equivalent to the polypeptide molecule of the present invention, for example, BLAST polypeptide search with score=50 and word length=3 may be carried out by the XBLAST program. In order to obtain gapped alignments for comparison, Gapped BLAST described in Altschul et al., (1997) Amino Acids Research 25(17): 3389-3402 can be utilized. In using BLAST and Gapped BLAST, the default parameters of the corresponding programs (e.g., XBLAST and NBLAST) can be used. In detail, see the World Wide Web (www) at ncbi.nlm.nih.gov. Another example of the mathematical algorithm that can be used for comparing sequences includes an algorithm described in Meyers and Miller (1988) Comput. Appl. Biosci. 4: 11-17. Such programs are incorporated into the ALIGN program that can be used for, for example, GENESTREAM network server (IGH Montpellier, FRANCE) or ISREC server. When the ALIGN program is used for comparison of the amino acid sequences, for example, PAM120 weight residue table can be used in which a gap length penalty is 12 and a gap penalty is 4. The identity between two amino acid sequences can be determined by using the GAP program in the GCG software package, using Blossom 62 matrix or PAM250 matrix with the gap weight of 12, 10, 8, 6, or 4, and the gap length weight of 2, 3, or 4.

(β-Galactosidase Gene)

The second aspect of the invention relates to a β-galactosidase gene. In one embodiment, the gene of the invention includes a DNA that encodes the amino acid sequence of SEQ ID NO: 6 or 7. A specific example of the embodiment is a DNA including the base sequence of SEQ ID NO: 5.

In general, when a part of DNA encoding a certain protein is modified, a protein encoded by the modified DNA may sometimes have the equal function to that of a protein encoded by the DNA before modification. That is to say, the modification of the DNA sequence does not have a substantial effect on the function of the encoded protein, so that the function of the encoded protein may be maintained before and after the modification. Thus, as another embodiment, the present invention provides DNA encoding a protein having a base sequence equivalent to the base sequence set forth in SEQ ID NO: 5 and having the β-galactosidase activity (hereinafter, which is also referred to as “equivalent DNA”). The “equivalent base sequence” herein denotes a base sequence which is partly different from the base sequence set forth in SEQ ID NO: 6 but in which the function (herein, β-galactosidase activity) of the protein encoded by the sequence is not substantially affected by the difference.

A specific example of the equivalent DNA includes DNA that hybridizes to the complementary base sequence of the base sequence of SEQ ID NO: 5 under stringent conditions. Herein, the “stringent conditions” are referred to as conditions in which a so-called specific hybrid is formed but a nonspecific hybrid is not formed. Such stringent conditions are known to persons skilled in the art. Such stringent conditions can be set with reference to, for example, Molecular Cloning (Third Edition, Cold Spring Harbor Laboratory Press, New York) and Current protocols in molecular biology (edited by Frederick M. Ausubel et al., 1987). An example of the stringent conditions can include a condition in which a hybridization solution (50% formamide, 10×SSC (0.15 M NaCl, 15 mM sodium citrate, pH 7.0), 5×Denhardt's solution, 1% SDS, 10% dextran sulfate, 10 μg/ml denatured salmon sperm DNA, and 50 mM phosphate buffer (pH 7.5)) is used and incubated at about 42° C. to about 50° C., thereafter, washed with 0.1×SSC and 0.1% SDS at about 65° C. to about 70° C. Further preferable stringent conditions can include, for example, a condition in which a hybridization solution 50% formamide, 5×SSC (0.15 M NaCl, 15 mM sodium citrate, pH 7.0), 1×Denhardt's solution, 1% SDS, 10% dextran sulfate, 10 μg/ml denatured salmon sperm DNA, and 50 mM phosphate buffer (pH 7.5)) is used.

Another specific example of the equivalent DNA can include DNA encoding a protein having a base sequence which includes substitution, deletion, insertion, addition or inversion in one or a plurality of bases (preferably one to several bases) when the base sequence of SEQ ID NO: 5 is a reference base sequence, and which has a β-galactosidase activity. The substitution, deletion, or the like, of the base may occur in a plurality of sites. The “plurality” herein denotes, for example, 2 to 40 bases, preferably 2 to 20 bases, and more preferably 2 to 10 bases, although it depends upon the positions or types of the amino acid residue in the three-dimensional structure of the protein encoded by the DNA. The above-mentioned equivalent DNA can be obtained by modifying DNA having the base sequence shown in SEQ ID NO: 5 so as to include substitution, deletion, insertion, addition and/or inversion of base by using treatment with a restriction enzyme; treatment with exonuclease, DNA ligase, etc; introduction of mutation by a site-directed mutagenesis (Molecular Cloning, Third Edition, Chapter 13, Cold Spring Harbor Laboratory Press, New York) and random mutagenesis (Molecular Cloning, Third Edition, Chapter 13, Cold Spring Harbor Laboratory Press, New York), and the like. Furthermore, the equivalent DNA can be also obtained by other methods such as irradiation with ultraviolet ray.

A further example of the equivalent DNA can include DNA having difference in base as mentioned above due to polymorphism represented by SNP (single nucleotide polymorphism).

Herein as shown in the examples mentioned below, the proteins (Gal2, Gal3 and Gal4) including the amino acid sequences of SEQ ID NO: 8 to SEQ ID NO: 10 that were each a fragment of the amino acid sequence (Gal1) of SEQ ID NO: 7 showed a high β-galactosidase activity. One embodiment of the invention based on this fact provides a β-galactosidase gene that encodes a protein including the amino acid sequence set forth in SEQ ID No. 7, or a fragment thereof, wherein changes of less than 60%, preferably less than 45%, and more preferably less than 25% are occurred in the amino acid sequence.

The gene of the present invention can be prepared in an isolated state by using a standard genetic engineering technique, a molecular biological technique, a biochemical technique, and the like, with reference to sequence information disclosed in the present specification or attached sequence list. Specifically, the gene of the present invention can be prepared by appropriately using oligonucleotide probe/primer capable of specifically hybridizing to the gene of the present invention from an appropriate genome DNA library or a cDNA library of Bacillus circulans, or cell body extract of Bacillus circulans. An oligonucleotide probe/primer can be easily synthesized by using, for example, a commercially available automated DNA synthesizer. As to a production method of libraries used for preparing the gene of the present invention, see, for example, Molecular Cloning, Third Edition, Cold Spring Harbor Laboratory Press, New York.

For example, a gene having the base sequence set forth in SEQ ID NO: 5 can be isolated by using a hybridization method using all or a part of the base sequence or its complimentary sequence as a probe. Furthermore, amplification and isolation can be carried out by using a nucleic acid amplification reaction (for example, PCR) using a synthesized oligonucleotide primer designed to specifically hybridize to a part of the base sequence. Furthermore, it is possible to obtain a target gene by chemical synthesis based on the information of the amino acid sequence set forth in SEQ ID NO: 6 or the base sequence set forth in SEQ ID NO: 5 (see, reference document: Gene, 60(1), 115-127 (1987)).

(Recombinant Vector)

Another aspect of the present invention relates to a recombinant vector containing the β-galactosidase gene of the present invention. The term “vector” as used in this specification is intended to refer to a nucleic acid molecule capable of transporting nucleic acid that is inserted in the vector to the inside of the target such as cells. The types or forms of vector are not particularly limited. Therefore, examples of the vector may be in a form of a plasmid vector, a cosmid vector, a phage vector, a viral vector (e.g., an adenovirus vector, an adeno-associated virus vector, a retrovirus vector, a herpes virus vector, etc).

According to the purpose of use (cloning, protein expression), and by considering the types of host cells, an appropriate vector is selected. Specific examples of the vector include a vector using Escherichia coli as a host (M13 phage or the modified body thereof, λ phage or the modified body thereof, pBR322 or the modified body thereof (pB325, pAT153, pUC8, etc.) and the like), a vector using yeast as a host (pYepSec 1, pMFa, pYES2, etc.), a vector using insect cells as a host (pAc, pVL, etc.), a vector using mammalian cells as a host (pCDM8, pMT2PC, etc.), and the like.

The recombinant vector of the present invention is preferably an expression vector. The term “expression vector” is a vector capable of introducing the nucleic acid inserted therein into the target cells (host cells) and being expressed in the cells. The expression vector usually includes a promoter sequence necessary for expression of the inserted nucleic acid and an enhancer sequence for promoting the expression, and the like. An expression vector including a selection marker can be used. When such an expression vector is used, by using the selection marker, the presence or absence of the introduction of an expression vector (and the degree thereof) can be confirmed.

Insertion of the gene of the present invention into a vector, insertion of the selection marker gene (if necessary), and insertion of a promoter (if necessary), and the like, can be carried out by a standard recombination DNA technology (see, for example, Molecular Cloning, Third Edition, 1.84, Cold Spring Harbor Laboratory Press, New York, a already-known method using restriction enzyme and DNA ligase).

(Transformant)

The present invention further relates to a transformant into which the gene of the present invention is introduced. In the transformant of the preset invention, the gene of the present invention exists as an exogenous molecule. Preferably, the transformant of the present invention can be preferably prepared by transfection or transformation using the vector of the present invention mentioned above. The transfection and transformation can be carried out by, for example, a calcium phosphate coprecipitation method, electroporation (Potter, H. et al., Proc. Natl. Acad. Sci. U.S.A. 81, 7161-7165(1984)), lipofection (Felgner, P. L. et al., Proc. Natl. Acad. Sci. U.S.A. 84,7413-7417 (1984)), microinjection (Graessmann, M. & Graessmann, A., Proc. Natl. Acad. Sci. U.S.A. 73,366-370 (1976)), a method by Hanahan (Hanahan, D., J. Mol. Biol. 166, 557-580 (1983)), a lithium acetate method (Schiestl, R. H. et al., Curr. Genet. 16, 339-346 (1989)), protoplast-polyethylene glycol method (Yelton, M. M. et al., Proc. Natl. Acad. Sci. 81, 1470-1474 (1984)), and the like.

The host cell is not particularly limited as long as the β-galactosidase of the invention can be expressed, and it can be selected from, for example, Bacillus genus bacteria (e.g., Bacillus subtillus, Bacillus likemiformis, Bacillus circulans, etc.), lactic acid bacteria (e.g., Lactococcus, Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, etc.), other bacteria (e.g. Escherichia, Streptomyces, etc.), yeast (e.g., Saccharomyces, Kluyveromyces, Candida, Torula, Torulopsis, etc.), and filamentous fungi (Eumycetes) (e.g., Aspergillus genus fungi such as Aspergillus oryzae and Aspergillus niger, Penicillium genus fungi, Trichoderma genus fungi, Fusarium genus fungi, etc.).

(Production of β-Galactosidase)

A further aspect of the invention is to provide a method for producing a β-galactosidase. In one embodiment of the production method of the invention, the β-galactosidase is produced by using the above-mentioned transformant. In the production method in this embodiment, the transformant is cultured under the conditions such that a protein encoded by a gene introduced therein is produced (step (1)). The culture conditions of transformant are known as to various vector-host systems, and a person skilled in the art can easily set an appropriate culture condition.

Culture methods and culture conditions are not particularly limited as long as the intended protein β-galactosidase can be produced. That is to say, methods and culture conditions suitable for culturing microorganisms to be used can be appropriately set to the conditions such that the β-galactosidase is produced. Liquid culture or solid culture may be employed as a culture method, but liquid culture is preferably used. The culture condition will be described with reference to a liquid culture as an example.

As the medium, any medium can be used as long as transformants to be used can grow. For example, a medium supplemented with a carbon source such as glucose, sucrose, gentiobiose, soluble starch, glycerin, dextrin, molasses, and organic acid; and further, a nitrogen source such as ammonium sulfate, ammonium carbonate, ammonium phosphate, ammonium acetate, or peptone, yeast extract, corn steep liquor, casein hydrolysate, bran, and meat extract; and furthermore, an inorganic salt such as potassium salt, magnesium salt, sodium salt, phosphate salt, manganese salt, iron salt, and zinc salt, and the like, can be used. In order to promote the growth of transformants to be used, vitamin, amino acid, and the like, may be added to the medium. The medium is cultured under the aerobic conditions such that the pH of the medium is adjusted to, for example, about 3 to 10 (preferably about 7 to 8), and the culture temperature is generally about 10° C. to 50° C. (preferably about 20° C. to 37° C.) for 1 to 7 days (preferably 3 to 4 days). An example of the culture method may include a shake culture method, and an aerobic submerged culture method by using a jar fermenter.

The produced protein (β-galactosidase) following the culturing step is collected (step (2)). When β-galactosidase is collected from the culture solution, the enzyme can be obtained by separation and purification by removing insoluble matters by, for example, filtration of culture supernatant, centrifugation, and the like, followed by carrying out an appropriate combination of concentration by ultrafiltration membrane, salting out by ammonium sulfate precipitation, dialysis, various types of chromatography of an ion-exchange resin, and the like. On the other hand, when β-galactosidase is collected from cell bodies, the target protein can be obtained by pulverizing the cell bodies by pressuring treatment, ultrasonic treatment, or the like, followed by separation and purification thereof similar to the above. After collection of the cell bodies from a culture solution by filtration, centrifugation, etc., a series of processes (pulverizing, separation, and purification of cell bodies) mentioned above may be carried out.

The purification degree of β-galactosidase is not particularly limited. Furthermore, the final form of the β-galactosidase may be a liquid state or a solid state (including a powdery state).

(Enzyme Preparation)

β-galactosidase of the present invention is provided in a form of, for example, an enzyme preparation. The enzyme preparation may contain, in addition to an active ingredient (β-galactosidase of the present invention), excipient, buffer agents, suspension agents, stabilizer, preservatives, antiseptics, physiologic saline, and the like. Examples of the excipient may include lactose, sorbitol, D-mannitol, sucrose, and the like. Examples of the buffer agent may include phosphate, citrate, acetate, and the like. Examples of the stabilizer may include propylene glycol, and ascorbic acid, and the like. Examples of the preservative may include phenol, benzalkonium chloride, benzyl alcohol, chlorobutanol, methyl paraben, and the like. Examples of the antiseptic may include benzalkonium chloride, parahydroxybenzoate, chlorobutanol, and the like.

In one embodiment of the enzyme preparations of the invention, one or more β-galactosidases as an active ingredient selected from the group consisting of a β-galactosidase including the amino acid sequence of SEQ ID NO: 7, a β-galactosidase including the amino acid sequence of SEQ ID NO: 8, a β-galactosidase including the amino acid sequence of SEQ ID NO: 9, and a β-galactosidase including the amino acid sequence of SEQ ID NO: 10 are used. In one embodiment, an enzyme preparation containing all these four kinds of β-galactosidases is provided.

(Use of β-Galactosidase)

A further aspect of the invention provides use of the β-galactosidase or enzyme preparation of the invention. Examples of such use are a production of a low-lactose milk, a production of a galacto-oligosaccharide which is an intestinal bifidobacterium growth factor, or a production of a medicine or supplement for patients with lactose intolerance. Lactose in raw materials can be reduced by using the β-galactosidase or enzyme preparation of the invention. For example, the low-lactose milk can be obtained by adding β-galactosidase of 1 U to a raw milk of 1 mL, and allowing the mixture at a low temperature of 10° C. so that the lactose is hydrolyzed. In the production of the galacto-oligosaccharide, β-galactosidase of 100 LU is added to a 40% lactose solution (pH 7.0) which has been dissolved by preheating and allowed to stand at 40° C. for 5 hours, thereby to produce the galacto-oligosaccharide, for example. Further, the galacto-oligosaccharide is represented by Gal-(Gal)n-Glc (n is usually 0 to 3) (Gal: galactose residue, Glc: glucose residue). The bond mode includes α1-3, and α1-6 other than β1-6, β1-3, β1-4, and β1-2.

Examples 1. Purification of β-Galactosidase Derived from Bacillus circulans (a) Measurement of β-Galactosidase Activity

In the following purification, a measurement of β-galactosidase activity was carried out by two kinds of methods such as (i) a method where 2-nitrophenyl-β-D-galactopyranoside (ONPG) was used as a substrate and (ii) a method where lactose was used as a substrate. Both methods were performed according to the method described in a non-patent document 1. In addition, the protein concentration was represented in terms of the absorbance at 280 nm.

i) ONPG Method

A 100 mM phosphate buffer solution (pH 6.0) 1.98 ml containing 0.245% ONPG was prewarmed at 40° C. for 10 minutes. After addition of a sample 20 μl to the buffer solution, the mixture was reacted at 40° C. for 10 minutes, and a 10% sodium carbonate solution 2.0 ml was added to stop the reaction. The absorbance of the reaction solution was measured at 420 nm, and β-galactosidase activity was calculated based on an activity of producing 1 μmol of 2-nitrophenol per one minute as 1 U.

ii) The Lactose Method

A 100 mM phosphate buffer solution (pH 6.0) 2 ml containing 5% lactose was prewarmed at 40° C. for 10 minutes. After addition of a sample 50 μl to the buffer solution, the mixture was reacted at 40° C. for 15 minutes, and boiled in a boiling bath to stop the reaction. Glucose concentration for the reaction solution of 100 μl was measured by the Glucostat method. That is, a 0.1N sodium hydroxide solution 100 μl was added to the reaction solution 100 μl, and the mixture was allowed to stand for one minute, and then 0.1N acetic acid and an acetate buffer solution (pH 5.0) 3 ml were added. To the solution was added a Glucostat solution (Ono Pharmaceutical Co., Ltd., Osaka, JAPAN) of 500 μl, and the increase rate of the absorbance at 550 nm was measured to calculate the lactose hydrolyzing activity when an activity of producing 1 μmol of glucose per one minute was defined as 1 U.

(b) Preparation of Crude Enzyme Powder of β-Galactosidase

Bacillus circulans ATCC 31382 was inoculated into a liquid culture medium containing 3.0% soy bean peptone, 2.5% meat extract, 1.0% yeast extract, and 0.5% lactose, and cultured under shaking at 30° C. for 3 days. After removal of the cell bodies by centrifuge, the resulting culture supernatant was treated with an ultrafiltration membrane (AIP-1013D, manufactured by Asahi Kasei Corporation, Tokyo, JAPAN) to obtain a 5-fold concentrate solution. The obtained concentrate was spray-dried to obtain a crude β-galactosidase enzyme powder.

(c) Purification of β-Galactosidase

A solution 50 ml obtained by dissolving the resulting crude enzyme powder in a 10 mM sodium phosphate buffer solution (pH 6.0) to a concentration of 5.0% was charged to a hydroxyapatite gel column (CHT™ Ceramic hydroxyapataite, manufactured by BIO-RAD Laboratories, Inc., Waltham, Mass., USA; 2.5 cm in inside diameter, 25 cm in length) which had been equilibrated with the same buffer solution, and unadsorbed proteins were eluted with a 10 mM sodium phosphate buffer solution (pH 6.0). After that, the enzyme was eluted by the stepwise elution method that changes the concentration of the sodium phosphate buffer in the order of 100 mM, 150 mM, 200 mM, 300 mM and 500 mM. This chromatography was performed at room temperature. As shown in FIG. 1, the enzyme showing a β-galactosidase (ONPG) activity was eluted with sodium phosphate buffer solution at a concentration of 100 mM, 150 mM, and 300 to 500 mM, and respective fractions were referred to as fraction 1, fraction 2, and fraction 3 in order. The enzyme contained in the fraction 3 was found to be an almost single protein with a molecular weight of 195 kDa as estimated by SDS-polyacrylamide gel electrophoresis and referred to as β-Gal1.

Then, the fraction 1 was separated and purified by an affinity chromatography. At first the fraction 1 was dialyzed against a 50 mM acetate buffer solution (pH 5.8). The dialyzed enzyme solution was charged to an affinity gel column (p-Aminobenzyl-1-thio-β-D-galactopyranoside-agarose, manufactured by Sigma-Aldrich (St. Louis, Mo., USA) 1.6 cm in diameter, 18 cm in length) which had been equilibrated with the same buffer solution, thereby to elute the unadsorbed protein with the same buffer solution. After that, elution was performed by a linear gradient method of changing the pH from 5.8 to 3.5 at 4° C. (50 mM acetate buffer solution (pH 5.8)/50 mM acetate buffer solution (pH 3.5)). As shown in the fraction 1, enzymes showing a β-galactosidase activity were eluted in a washing fraction and at about pH 4.4, respectively. They showed a nearly single band in SDS-polyacrylamide gel electrophoresis and a molecular weight of 135 kDa and 86 kDa, respectively. The former was referred to as β-Gal2, and the latter was referred to as β-Gal3.

On the other hand, fraction 2 was separated and purified by an affinity chromatography in a similar manner to the fraction 1. The fraction 2 was dialyzed against a 50 mM acetate buffer solution (pH 5.8), and charged to the above affinity gel column which had been equilibrated with the same buffer solution. As in FIG. 2, unadsorbed proteins were eluted with the same buffer solution, and then elution was performed by a linear gradient method of changing the pH from 5.8 to 3.5 at 4° C. As shown in FIG. 3, enzymes each showing a β-galactosidase activity were eluted in a washing fraction and at about pH 4.4, respectively. They showed a nearly single band in SDS-polyacrylamide gel electrophoresis and a molecular weight of 86 kDa and 160 kDa, respectively. The former was the same as β-Gal3 and the latter was referred to as β-Gal4. FIG. 4 shows the analytical result of 10% SDS-PAGE of crude enzyme sample (lane 2) as well as purified β-Gal1 (lane 3), β-Gal2 (lane 4), β-Gal3 (lane 5), and β-Gal4 (lane 6).

2. Various Properties of Purified β-Galactosidase Derived from Bacillus circulans

The main properties of four kinds of purified β-galactosidases were examined.

(a) Measurement of Specific Activity

An activity when ONPG (final concentration of 0.24%) and lactose (final concentration of 4.88%) were used as a substrate was measured in a 100 mM phosphate buffer solution (pH 6) at 40° C. The results are shown in Table 1. In addition, when ONPG was used as a substrate, an enzyme amount to produce a product, nitrophenol, 1 μmol in one minute under the conditions of 40° C. and pH 6 was defined as 1 U, and when lactose was used as a substrate, an enzyme amount to produce a product, glucose, 1 μmol in one minute under the conditions of 40° C. and pH 6 was defined as 1 U. As shown in Table 1, it is understood that β-Gal1 has a higher hydrolyzing activity against ONPG than lactose, while β-Gal2, 3-Gal3 and β-Gal4 each shows a lower hydrolyzing activity against ONPG than lactose. “GNSVSYDGERRVNFNEN” recited in Table 1 corresponds to SEQ ID NO: 1 and “SVSYDGERRVNFNEN” recited in Table 1 corresponds SEQ ID NO: 17.

TABLE 1 Crude enzyme β-Gal1 β-Gal2 β-Gal3 β-Gal4 Enzyme (U/mg) (U/mg) (U/mg) (U/mg) (U/mg) Specific activity 16.0 50.0 13.4 17.6 10.9 (Substrate; ONPG) Specific activity 35.4 46.5 62.0 72.6 45.0 (Substrate; lactose) Molecular weight — 189.283 kDa 134.788 kDa 91.027 kDa 153.932 kDa (SDS-PAGE) (195 kDa) (135 kDa) (86 kDa) (160 kDa) N-Terminal amino — GNSVSYDGERRVNFNEN Same as the left Same as the left Same as the left acid sequence (SVSYDGERRVNFNEN)

(b) Determination of Molecular Weight

The molecular weights of four kinds of β-galactosidases were determined using a MALDI (Matrix Assisted Laser Desorption/Ionization) analyzer. As a sample, a mixed solution of 0.1 μl of 10 mg/ml Sinapinic acid/0.1 μl of 0.7 to 3 mg/ml enzyme solution was used. As a result, β-Gal1 was found to be 189.283 kDa, β-Gal2 was found to be 134.788 kDa, β-Gal3 was found to be 91.027 kDa, and β-Gal4 was found to be 153.932 kDa (see Table 1). In addition, the molecular weights determined by SDS-polyacrylamide gel electrophoresis (FIG. 4) were shown in parentheses in Table 1. The molecular weights that were determined with a mass spectrometer for any enzymes showed a similar result to the molecular weights that were determined from SDS-polyacrylamide gel electrophoresis.

(c) Determination of N-Terminal Amino Acid Sequence

Analysis of the N-terminal amino acid sequence of each of four kinds of β-galactosidases was performed using a protein sequencer. As a result, it was revealed that two kinds of sequences, i.e. GNSVSYDGERRVNFNEN (SEQ ID NO: 1) and SVSYDGERRVNFNEN (SEQ ID NO: 17) were included in β-Gal1. However, the difference between these two amino acid sequences resides in the presence or absence of GN in the N-terminal, and their amino acid sequences were found to be basically the same from each other. Moreover, the N-terminal amino acid sequence of each of β-Gal2, 3-Gal3, and β-Gal4 was similar to that of β-Gal1.

(d) Determination of Internal Amino Acid Sequence

Then, each purified enzyme of β-Gal1, β-Gal2, and β-Gal3 was prepared to 1 to 2 mg/mL, and trypsin (0.5 mg/mL) was added to this, followed by incubation at 37° C. After 48 hours, these enzymes were subjected to a 8% SDS-polyacrylamide gel electrophoresis. A band of 70 kDa was detected from all of such enzymes. The gel after the electrophoresis was transferred to a nitrocellulose membrane for staining with Coomassie Brilliant Blue. A band of 70 kDa derived from each enzyme was cut out from the stained bands, and the amino acid sequence was analyzed by a protein sequencer. As a result, the amino acid sequences of the N-terminal 5 residues of the 70 kDa proteins derived from each enzyme were matched each other. In addition, the amino acid sequence of the N-terminal 15 residues of the 70 kDa protein derived from β-Gal3 was found to be EDRADVNIKTKISND (SEQ ID NO: 2).

3. Acquisition of Gene Fragment Encoding β-Galactosidase Derived from Bacillus circulans (a) Isolation of Chromosomal DNA

A chromosomal DNA was prepared from the cell bodies of Bacillus circulans ATCC 31382 by the Saito/Miura method (non-patent document 5).

(b) Production of DNA Probe by PCR

Based on the N-terminal amino acid sequence and the internal amino acid sequence, which were determined in the above 2., two kinds of oligonucleotides (SEQ ID NO: 3 and SEQ ID NO: 4) were synthesized and served as a PCR primer. Using these primers, a PCR reaction was performed with a chromosomal DNA of Bacillus circulans as a template under the following conditions.

<PCR Reaction Solution>

-   10×PCR reaction buffer solution (Takara Bio Inc., Shiga, JAPAN) 5.0     μl -   dNTP mixture (2.5 mM each, Takara Bio Inc., Shiga, JAPAN) 8.0 μl -   25 mM MgCl₂ 5.0 μl -   50 μM sense primer 0.5 μl -   50 μM antisense primer 0.5 μl -   Distilled water 29.5 μl -   Chromosomal DNA solution (100 μg/mL) 1.0 μl -   LA Taq DNA polymerase (Takara Bio Inc., Shiga, JAPAN) 0.5 μl

<PCR Reaction Conditions>

-   Stage 1: Denaturation (95° C., 5 minutes) 1 cycle -   Stage 2: Denaturation (95° C., 1 minute) 30 cycles -   Annealing (52° C., 1 minute) -   Extension (72° C., 1 minute) -   Stage 3: Extension (72° C., 10 minutes) 1 cycle

After cloning of the obtained DNA fragment of about 0.6 kb into pGEM®-Teasy (Promega, Madison, Wis., USA), identification of the base sequence revealed that a base sequence to encode the partial amino acid sequence mentioned above was found just after a sense primer and just before an antisense primer. This DNA fragment was served as a DNA probe for full length gene cloning.

(c) Construction of Gene Library

As a result of Southern hybridization analysis of the chromosomal DNA derived from Bacillus circulans, a single band of about 8.2 kb that hybridizes to a probe DNA was found in the hydrolysate by SpeI. For cloning of this SpeI DNA fragment of about 8.2 kb, a gene library was constructed as follows. The chromosomal DNA prepared in (a) mentioned above was treated with SpeI. The chromosomal DNA 50 vg, 10×M buffer solution 40 μl, distilled water 342.0 μl and SpeI 8.0 μl were mixed together, and treated at 37° C. for 15 hours. The resulting hydrolysate was ligated to SpeI-digested pBluescript II KS+vector (Stratagene, La Jolla, Calif., USA) to obtain a gene library.

(d) Screening of Gene Library

The 0.6 kb DNA fragment obtained in the above (b) was labeled with DIG-High Prime (Roche, Basel, SWITZERLAND). Using this labeled product as a DNA probe, the gene library obtained in the above (c) was screened by a colony hybridization method. A plasmid pBlue-Gal1 was obtained from the resulting positive colony.

(e) Determination of Base Sequence

The base sequence of the plasmid pBlue-Gal1 was determined according to the usual method. The base sequence (5214 bp) that encodes a β-galactosidase derived from Bacillus circulans is shown in SEQ ID NO: 5. In addition, the amino acid sequence (1738 amino acids) that is encoded by SEQ ID NO: 5 is shown in SEQ ID NO: 6. In this amino acid sequence, the N-terminal region amino acid sequence (SEQ ID NO: 1) and the internal amino acid sequence (SEQ ID NO: 2) which were determined in the above 2, were found. Interestingly, the initiation codon in the present gene was thought to be GTG. Moreover, an amino acid sequence that excludes the signal peptide from the amino acid sequence of SEQ ID NO: 6 is shown in SEQ ID NO: 7.

4. Expression of β-Galactosidases β-Gal1, β-Gal2, and β-Gal4 Derived from Bacillus circulans in Escherichia coli

(a) Construction of Expression Plasmid in Escherichia coli for β-Galactosidase

Since the N-terminal region amino acid sequences of the proteins corresponding to β-Gal1, β-Gal2, and β-Gal4 each having a molecular weight of 189.3 kDa, 134.8 kDa, and 153.9 kDa respectively (values by mass spectrometry) are common among them, a certain oligonucleotide F-Gal (SEQ ID NO: 11) was synthesized based on the DNA sequence to encode such an amino acid sequence. In addition, based on the DNA sequence to encode an each deduced C-terminal region amino acid sequence, three kinds of oligonucleotides R-Gal1, R-Gal2, and R-Gal4 (SEQ ID NO: 12 to SEQ ID NO: 14, respectively) were synthesized and they were served as a PCR primer. A SaII restriction enzyme recognition site was added to the sense primer F-Gal, and a SaII restriction enzyme recognition site was added to the antisense primers R-Gal1, R-Gal2, and R-Gal4. Using these primers and a chromosomal DNA having a β-galactosidase gene as a template, a PCR reaction was performed under the following conditions.

<PCR Reaction Solution>

-   10×PCR reaction buffer solution (TOYOBO Co., Ltd., Osaka, JAPAN) 5.0     μl -   dNTP mixture (2.5 mM each, TOYOBO Co., Ltd., Osaka, JAPAN) 5.0 μl -   10 μM sense primer 1.5 μl -   10 μM antisense primer 1.5 μl -   25 mM MgSO₄ 2.0 μl -   Distilled water 33.0 μl -   Chromosomal DNA solution (200 μg/ml) 1.0 μl -   KOD-Plus-DNA polymerase (TOYOBO Co., Ltd., Osaka, JAPAN) 1.0 μl

<PCR Reaction Conditions>

-   Stage 1: Denaturation (94° C., 2 minutes) 1 cycle -   Stage 2: Denaturation (94° C., 15 seconds) 30 cycles -   Annealing (57° C., 30 seconds) -   Extension (68° C., 5 minutes)

The obtained PCR products were confirmed by the electrophoresis, and desalinated (69 μl) by the ethanol precipitation method. Subsequently, 10×T buffer solution of 15 μl, 0.1% BSA solution of 10 μl, SaII 3 μl, and SaII 3 μl were added to the PCR products, followed by enzymatic treatment at 37° C. for 15 hours. The solution digested with the restriction enzymes was confirmed by the electrophoresis, purified with NucleoSpin® Extract II (NIPPON Genetics Co., Ltd., Tokyo, JAPAN), and β-Gal1, β-Gal2, and β-Gal4 fragments were ligated to a vector pCold II DNA (Takara Bio Inc., Shiga, JAPAN) which had been treated beforehand with SadI and SaII, thereby to obtain expression plasmids pCold-Gal1, pCold-Gal2, and pCold-Gal4.

(b) Expression of β-Galactosidase in Escherichia coli

The expression plasmids pCold-Gal1, pCold-Gal2, and pCold-Gal4 were each introduced into Escherichia coli BL21 Competent Cells (Takara Bio Inc., Shiga, JAPAN). The strains bearing respectively the pCold-Gal1, pCold-Gal2, and pCold-Gal4 into which a target β-galactosidase gene was inserted were selected by colony PCR from the transformants obtained as ampicillin-resistant strains. In addition, a transformant of Escherichia coli BL21 having an expression vector pCold II DNA as a control was also obtained. These transformants were inoculated to an LB medium 1 ml containing ampicillin of 100 μg/mL and cultured until reaching O.D600=0.4 to 1.0 at 37° C. and 170 rpm (previous culture). Subsequently, the preculture solution 300 μl was inoculated to an LB medium 9 ml containing ampicillin of 100 μg/mL and cultured until reaching O.D600=0.4 to 1.0 at 37° C. and 170 rpm. After allowing the culture solution to stand at 15° C. for 30 minutes, 0.1M IPTG 9 μl was added thereto, and culturing (mainculture) was performed at 15° C. and 160 rpm for 24 hours, after which time the cell bodies were collected. The cell bodies were suspended in 100 mM phosphate buffer solution (pH 6.0) 1.0 ml, 0.1 mm glass beads 0.50 g were added, and the cell bodies were disrupted with a multi-beads shocker (Yasui Kikai Corporation, Osaka, JAPAN). The disruption condition was as follows: 3.75 cycles of ON 120 seconds and OFF 60 seconds were repeated. The resulting cell-free extract was centrifuged to obtain a soluble component.

(c) Confirmation of β-Galactosidase Expression

The obtained soluble component was subjected to SDS-PAGE. PhastSystem™ (GE Healthcare, Little Chalfont, UK) was used as an electrophoresis device and PhastGel™ Homogeneous 7.5 (GE Healthcare, Little Chalfont, UK) was used as a separation gel. As a result, it was confirmed as shown in FIG. 5 that significant proteins which were considered to be β-Gal1, 3-Gal2, and β-Gal4 respectively were produced in the vicinity of 189 kDa for pCold-Gal1, in the vicinity of 135 kDa for pCold-Gal2, and in the vicinity of 154 kDa for pCold-Gal4. In the case of pCold II DNA as a control, a similar protein production was not confirmed and it was thought that these proteins depended on respective introduction of β-galactosidase genes such as β-Gal1, β-Gal2, and β-Gal4.

In addition, a β-galactosidase activity was measured on the same sample using each of ONPG and lactose as a substrate. The results of the activity measurement are shown in Table 2.

TABLE 2 ONPG-hydrolyzing activity Lactose-hydrolyzing activity (U/mg) (U/mg) pColdII-Gal1 31.99 34.19 pColdII-Gal2 6.40 26.43 pColdII-Gal4 2.13 8.74 pColdII 0.48 0.00

In any case, if ONPG was used as a substrate, a β-galactosidase activity that was four or more times greater than the activity of the control was detected, and if lactose was used as a substrate, the apparent β-galactosidase activity was detected in comparison with the control. An expression of the target β-galactosidases β-Gal1, β-Gal2, and β-Gal4 were confirmed.

5. Expression of β-Galactosidase β-Gal3 Derived from Bacillus circulans in Escherichia coli

(a) Construction of Expression Plasmid for β-Galactosidase in Escherichia coli

In the same manner as above, an expression plasmid for β-Gal3 was constructed. Based on the DNA sequence to encode an N-terminal region amino acid sequence and a deduced C-terminal region amino acid sequence of the protein corresponding to β-Gal3 with a molecular weight of 91.0 kDa (the value as estimated by mass spectrometry), two kinds of oligonucleotides (SEQ ID NO: 15 and SEQ ID NO: 16) were synthesized and they were served as a PCR primer. An NdeI restriction enzyme recognition site was added to the sense primer F-Gal3, and an XbaI restriction enzyme recognition site was added to the antisense primer R-Gal3. Using these primers and a chromosomal DNA having a β-galactosidase gene as a template, a PCR reaction was performed under the following conditions.

<PCR Reaction Solution>

-   10×PCR reaction buffer solution (TOYOBO Co., Ltd., Osaka, JAPAN) 5.0     μl -   dNTP mixture (2.5 mM each, TOYOBO Co., Ltd., Osaka, JAPAN) 5.0 μl -   10 μM sense primer 1.5 μl -   10 μM antisense primer 1.5 μl -   25 mM MgSO₄ 2.0 μl -   Distilled water 33.0 μl -   Chromosomal DNA solution (200 μg/ml) 1.0 μL -   KOD-Plus-DNA polymerase (TOYOBO Co., Ltd., Osaka, JAPAN) 1.0 μL

<PCR Reaction Conditions>

-   Stage 1: Denaturation (94° C., 2 minutes) 1 cycle -   Stage 2: Denaturation (94° C., 15 seconds) 30 cycles -   Annealing (57° C., 30 seconds) -   Extension (68° C., 3 minutes)

The obtained PCR products were confirmed by the electrophoresis, then and desalinated (84 μl) by the ethanol precipitation method. Subsequently, a suitable buffer solution of 10 μl as well as NdeI 3 μl and XbaI 3 μl were added to the PCR products, followed by enzymatic treatment at 37° C. for 15 hours. The solution digested with the restriction enzymes was confirmed by the electrophoresis, purified with NucleoSpin® Extract II (NIPPON Genetics Co., Ltd., Tokyo, JAPAN), and then ligated to a vector pCold III DNA which had been treated beforehand with NdeI and XbaI, thereby to obtain an expression plasmid pCold-Gal3.

(b) Expression of β-Galactosidase in Escherichia coli

The expression plasmid pCold-Gal3 was introduced into Escherichia coli BL21 Competent Cells. A strain bearing pCold-Gal3 into which a target β-galactosidase gene was inserted was selected by colony PCR from the transformants obtained as ampicillin-resistant strains. In addition, a transformant of Escherichia coli BL21 having an expression vector pCold III DNA as a control was also obtained. These transformants were inoculated to an LB medium 1 ml containing ampicillin of 100 μg/mL and cultured until reaching O.D600=0.4 to 1.0 at 37° C. and 170 rpm (previous culture). Subsequently, the preculture solution 300 μl was inoculated to an LB medium 9 ml containing ampicillin of 100 μg/mL and cultured until reaching O.D600=0.4 to 1.0 at 37° C. and 170 rpm. After treatment of the culture solution at 15° C. for 30 minutes, 0.1M IPTG 9 μl was added thereto, and culturing (mainculture) was performed at 15° C. and 160 rpm for 24 hours, after which time the cell bodies were collected. The cell bodies were suspended in 100 mM phosphate buffer solution (pH 6.0) 1.0 ml, φ0.1 mm glass beads 0.50 g were added, and the cell bodies were disrupted with a multi-beads shocker. The disruption condition was as follows: 3.75 cycles of ON 120 seconds and OFF 60 seconds were repeated. The resulting cell-free extract was centrifuged to obtain a soluble component.

(c) Confirmation of β-Galactosidase Expression

The soluble component obtained in the same manner as in 4, was subjected to SDS-PAGE. PhastSystem™ (GE Healthcare, Little Chalfont, UK) was used as an electrophoresis device and PhastGel™ Homogeneous 7.5 (GE Healthcare, Little Chalfont, UK) was used as a separation gel. As a result, as shown in FIG. 5, a significant production of a protein that was considered to be β-Gal3 was confirmed in the vicinity of 91 kDa for pCold-Gal3. In the case of pCold III DNA as a control, a similar protein production was not confirmed and thus it was thought that the protein depended on the introduction of β-galactosidase gene β-Gal3.

In addition, a β-galactosidase activity was measured on the same sample using each of ONPG and lactose as a substrate. The measurement results of the activity are shown in Table 3. A β-galactosidase activity that was five or more times greater than the activity of the control was detected when ONPG was used as a substrate, and a β-galactosidase activity that was 200 or more times greater than the activity of the control was detected when lactose was used as a substrate. An expression of the target β-galactosidase β-Gal3 was confirmed.

TABLE 3 ONPG-hydrolyzing Lactose-hydrolyzing activity (U/mg) activity (U/mg) pColdIII-Gal3 1.79 6.01 pColdIII 0.34 0.03

INDUSTRIAL APPLICABILITY

The present invention provides a novel β-galactosidase derived from Bacillus circulans. The β-galactosidase of the invention is industrially useful and can be used, for example, in the production of milk, dairy products, fermented dairy products, galacto-oligosaccharides or supplements for foods.

The present invention is not limited at all to the description of the above embodiments and Examples. A variety of modifications, which should not depart from the scope of the claims and which can be easily conceived by a person skilled in the art, are included in the invention.

Contents of the theses, unexamined patent publications, examined patent publications, and other published documents referred to in this specification are herein incorporated by reference in their entirety.

[Sequence List Free Text] SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 11 to SEQ ID NO: 16: Description of Artificial Sequence: Primer SEQUENCE LISTING 

1. A method for producing a product selected from the group consisting of a low-lactose milk, a galacto-oligosaccharide that is an intestinal bifidobacterium growth factor, and a medicine or supplement for patients with lactose intolerance, comprising a step to make a β-galactosidase enzyme act, wherein the β-galactosidase comprises a polypeptide selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, a polypeptide having at least 90% identity to SEQ ID NO: 7, a polypeptide having at least 90% identity to SEQ ID NO: 8, a polypeptide having at least 90% identity to SEQ ID NO: 9, and a polypeptide having at least 90% identity to SEQ ID NO:
 10. 2. The method of claim 1, wherein the polypeptide has at least 95% sequence identity to SEQ ID NOs: 7, 8, 9, or
 10. 3. The method of claim 1, wherein the polypeptide has at least 98% sequence identity to SEQ ID NOs: 7, 8, 9, or
 10. 4. The method of claim 1, wherein the polypeptide has at least 99% sequence identity to SEQ ID NOs: 7, 8, 9, or
 10. 5. A method for producing a product selected from the group consisting of a low-lactose milk, a galacto-oligosaccharide that is an intestinal bifidobacterium growth factor, and a medicine or supplement for patients with lactose intolerance, comprising a step to make an enzyme preparation comprising a mixture of isolated β-galactosidase enzymes obtained from Bacillus circulans act, wherein the mixture of enzymes comprises enzymes selected from the group consisting of SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, a polypeptide having at least 90% identity to SEQ ID NO: 8, a polypeptide having at least 90% identity to SEQ ID NO: 9, and a polypeptide having at least 90% identity to SEQ ID NO: 10, wherein SEQ ID NO: 8, SEQ ID NO: 9, and SEQ ID NO: 10 are c-terminus truncations of native β-galactosidase, and wherein the enzymes have decreased p-nitrophenyl-β-D-galactopyranoside (ONPG) hydrolyzing activity relative to the native β-galactosidase and/or increased lactose hydrolyzing activity relative to native β-galactosidase.
 6. The method of claim 5, wherein the polypeptide has at least 95% sequence identity to SEQ ID NOs: 8, 9, or
 10. 7. The method of claim 5, wherein the polypeptide has at least 98% sequence identity to SEQ ID NOs: 8, 9, or
 10. 8. The method of claim 5, wherein the polypeptide has at least 99% sequence identity to SEQ ID NOs: 8, 9, or
 10. 9. The method of claim 5, wherein each of the enzyme has an increased lactose hydrolyzing activity relative to the native β-galactosidase. 